- a -

• a : Sequence::stateCounter
• abv : Sequence::node

- b -

• beg : Sequence::marginal

- c -

• c : Sequence::stateCounter
• chisquareds : Sequence::HKAresults

- d -

• D : Sequence::HKAdata
• duplicate : Sequence::samflag

- f -

• fhat : Sequence::HKAresults
• first_read : Sequence::samflag
• flag : Sequence::samflag

- g -

• g : Sequence::stateCounter
• gap : Sequence::stateCounter

- i -

• is_paired : Sequence::samflag
• is_proper_pair : Sequence::samflag

- m -

• mate_unmapped : Sequence::samflag
• mstrand : Sequence::samflag

- n -

• n : Sequence::stateCounter
• nA : Sequence::HKAdata
• ndna : Sequence::stateCounter
• nnodes : Sequence::marginal
• not_primary : Sequence::samflag
• nsam : Sequence::marginal
• nsegs : Sequence::chromosome

- o -

• one : Sequence::stateCounter

- p -

• pop : Sequence::chromosome

- q -

• qcfail : Sequence::samflag
• qstrand : Sequence::samflag
• query_unmapped : Sequence::samflag

- s -

• SA : Sequence::HKAdata
• second_read : Sequence::samflag
• segs : Sequence::chromosome

- t -

• t : Sequence::stateCounter
• That : Sequence::HKAresults
• thetas : Sequence::HKAresults
• time : Sequence::node
• tree : Sequence::marginal

- x -

• xsq : Sequence::HKAresults
• xsqA : Sequence::HKAresults
• xsqB : Sequence::HKAresults

- z -

• zero : Sequence::stateCounter